The purpose of this model is to understand how genetic architectures of alternative reproductive tactics impact their maintenance in populations. I’m using an individual-based simulation model with different selection scenarios, types of alternative tactics, and genetic architectures (genome-wide additive genetic variance, supergenes, expression networks).
Males can be courters or not-courters and parents or not-parents. When the model is run with both traits, this results in four possible morphs: courter/parent, courter/not-parent, not-courter/parent, and not-courter/not-parent. Generations are non-overlapping and there is one reproductive bout per generation. In each generation, the population follows the following timeline:
Fig. 1 Flowchart of simulation
each step is explained in further detail below.
A female samples 50 males and chooses a male to nest with based on his courtship trait. If there are no courtship traits in the model, she chooses based on the male’s parental trait. If she does not encouter an acceptable male, she does not nest. If she encounters multiple equally-acceptable males, she randomly selects one of them.
Once a female decides to nest, up to three males can fertilize the nest. Courters and parental males can contribute more sperm than non-courter and non-parental males: \(r_{courter}=r_{parent}=8\) and \(r_{non-courter}=r_{non-parent}=4\). A courter/non-parent has \(r_{non-parent}\) and a non-courter/parent has \(r_{parent}\). The male with whom the female is nesting gets \(r_{parent}/\Sigma{n_{sperm}}\) and additional non-parental males (up to 2) get \((r_{non-parent}*0.5/\Sigma{n_{sperm}})\), where \(\Sigma{n_{sperm}}\) is the total number of sperm contributed by all of the males, weighted by the sperm competition factor (0.5 is the default for all males except the nesting male). So, when a female mates with one courter and two non-parentals, \(\Sigma{n_{sperm}}\) = \(r_{courter}\) + 2\(*\)(0.5\(*\)\(r_{sneaker}\)), where \(r_{courter}\) = 8 and \(r_{sneaker}\) = 4, therefore \(\Sigma{n_{sperm}}\) = 12.
That being said, every time a male mates he uses his sperm, so after one mating where a courter fertilizes 50% of the female’s 4 eggs, he only has 6 sperm for his next mating.
Before the babies can survive, the nest has to survive. This step is only relevant when parental traits are in the model - if only the courtship trait is specified, then all progeny in the nest survive at this point. When males have the parental trait, if the female has given eggs to a non-parental male (because she chose based on courtship traits), then the nest has a 10% chance of surviving. If the female has given eggs to a parental male, the nest has a 90% chance of surviving.
Once the identities of the surviving nests are known–along with the identities of the parents, including sneaker parents–the offspring are created in the simulation. The offspring are created to fill the full carrying capacity of the population, with the numbers per nest being equally divided among all surviving offspring. This allows the population to maintain a constant population size (prior to viability selection) while maintaining the relative successes of the given genotypes/morphs.
Before becoming adults, the offspring experience viability selection. Courters and parental males are disfavored in viability selection, with a survival probability of 0.9950125. If an individual is both a courter and a parental male, the survival probability is 0.9900498. Non-courters and non-parental males have survival probabilities of 1.
After 10000 generations, I begin tracking the change in frequency of the courter and parent traits, and do so for 2000 additional generations. I calculate the variance in the change in frequency over those 2000 generations. I declare an equilibrium (‘stasis’) has been reached if the last change in frequency of both traits is less than the variance in changes in frequency.
In these cases, the traits are encoded by a number (50) of loci, whose alleles contribute additively to determine the trait value. These alleles are all freely recombining and are not adhered to any physical genomic location (aka this is a classical quantitative genetics approach). The overall trait value is compared to a population-level threshold (which is static, in these cases), and if the trait value is above the threshold the male takes the parent or courter morph and if it is below he does not. Below, I’m showing the results from 10 replicates of each scenario.
Females choose nests based on whether the male is a courter or not, and they all prefer courters all of the time (the female preference does not have a genetic basis and does not evolve). The only way that non-courters produce offspring is through sneaking, but all males can be sneakers (both courters and non-courters). Because parental care is not incorporated in this model, all nests survive.
Frequency of the courter morph with unlinked additive genetic variances (each color represents a different replicate)
Of the 20 replicates, 20 reached a steady state by 10000 generations. The different runs all overlap, suggesting that they all converge on the same outcome: all males are courters. This result is also obvious by inspecting a table of courter frequencies and fitnesses in the final generation of the runs.
| CourterFreq | CourterW | NonCourterW | |
|---|---|---|---|
| courter_unlinked_1_summary.txt_1 | 1 | 2.13675 | 0 |
| courter_unlinked_1_summary.txt_2 | 1 | 2.03666 | 0 |
| courter_unlinked_1_summary.txt_3 | 1 | 2.06186 | 0 |
| courter_unlinked_1_summary.txt_4 | 1 | 2.03252 | 0 |
| courter_unlinked_2_summary.txt_1 | 1 | 2.13675 | 0 |
| courter_unlinked_2_summary.txt_2 | 1 | 2.03666 | 0 |
| courter_unlinked_2_summary.txt_3 | 1 | 2.06186 | 0 |
| courter_unlinked_2_summary.txt_4 | 1 | 2.03252 | 0 |
| courter_unlinked_3_summary.txt_1 | 1 | 2.13675 | 0 |
| courter_unlinked_3_summary.txt_2 | 1 | 2.03666 | 0 |
| courter_unlinked_3_summary.txt_3 | 1 | 2.06186 | 0 |
| courter_unlinked_3_summary.txt_4 | 1 | 2.03252 | 0 |
| courter_unlinked_4_summary.txt_1 | 1 | 1.95303 | 0 |
| courter_unlinked_4_summary.txt_2 | 1 | 2.04723 | 0 |
| courter_unlinked_4_summary.txt_3 | 1 | 2.02857 | 0 |
| courter_unlinked_4_summary.txt_4 | 1 | 2.07708 | 0 |
| courter_unlinked_5_summary.txt_1 | 1 | 1.95303 | 0 |
| courter_unlinked_5_summary.txt_2 | 1 | 2.04723 | 0 |
| courter_unlinked_5_summary.txt_3 | 1 | 2.02857 | 0 |
| courter_unlinked_5_summary.txt_4 | 1 | 2.07708 | 0 |
We may also be interested in the evolution of the courter trait values, which reflects the additive effects of all loci.
Evolution of courtship trait with unlinked loci
Frequency of the courter morph with unlinked additive genetic variances and without viability selection (each color represents a different replicate)
Of the 20 replicates, 20 reached a steady state by 10000 generations. The different runs all overlap, suggesting that they all converge on the same outcome: all males are courters. This result is also obvious by inspecting a table of courter frequencies and fitnesses in the final generation of the runs.
| CourterFreq | CourterW | NonCourterW | |
|---|---|---|---|
| courter_unlinked_novs_1_summary.txt_1 | 1 | 2.00401 | 0 |
| courter_unlinked_novs_1_summary.txt_2 | 1 | 2.13220 | 0 |
| courter_unlinked_novs_1_summary.txt_3 | 1 | 2.02020 | 0 |
| courter_unlinked_novs_1_summary.txt_4 | 1 | 2.13220 | 0 |
| courter_unlinked_novs_2_summary.txt_1 | 1 | 2.00401 | 0 |
| courter_unlinked_novs_2_summary.txt_2 | 1 | 2.13220 | 0 |
| courter_unlinked_novs_2_summary.txt_3 | 1 | 2.02020 | 0 |
| courter_unlinked_novs_2_summary.txt_4 | 1 | 2.13220 | 0 |
| courter_unlinked_novs_3_summary.txt_1 | 1 | 2.00401 | 0 |
| courter_unlinked_novs_3_summary.txt_2 | 1 | 2.13220 | 0 |
| courter_unlinked_novs_3_summary.txt_3 | 1 | 2.02020 | 0 |
| courter_unlinked_novs_3_summary.txt_4 | 1 | 2.13220 | 0 |
| courter_unlinked_novs_4_summary.txt_1 | 1 | 2.05339 | 0 |
| courter_unlinked_novs_4_summary.txt_2 | 1 | 2.04918 | 0 |
| courter_unlinked_novs_4_summary.txt_3 | 1 | 1.96078 | 0 |
| courter_unlinked_novs_4_summary.txt_4 | 1 | 1.96850 | 0 |
| courter_unlinked_novs_5_summary.txt_1 | 1 | 2.05339 | 0 |
| courter_unlinked_novs_5_summary.txt_2 | 1 | 2.04918 | 0 |
| courter_unlinked_novs_5_summary.txt_3 | 1 | 1.96078 | 0 |
| courter_unlinked_novs_5_summary.txt_4 | 1 | 1.96850 | 0 |
We may also be interested in the evolution of the courter trait values, which reflects the additive effects of all loci.
Evolution of courtship trait with unlinked loci and no viability selection
In this case, there are no courtship traits so females lay eggs in nests randomly. Non-parental males will sneak fertilizations in parental males’ nests. Parental males provide care that allows nests to have a 90% chance of survival. The female preference does not have a genetic basis and does not evolve.
Frequency of parent morph with unlinked loci (each color represents a different replicate)
Again, inference is facilitated by looking at the final frequencies and fitnesses in each replicate:
| ParentFreq | ParentW | NonParentW | |
|---|---|---|---|
| parent_unlinked_1_summary.txt_1 | 1.2478800 | 1.57238 | 1.000000 |
| parent_unlinked_1_summary.txt_2 | 1.2094800 | 1.65707 | 0.586667 |
| parent_unlinked_1_summary.txt_3 | 1.2352000 | 1.65618 | 0.903846 |
| parent_unlinked_1_summary.txt_4 | 1.2041800 | 1.67285 | 0.753846 |
| parent_unlinked_2_summary.txt_1 | 1.2478800 | 1.57238 | 1.000000 |
| parent_unlinked_2_summary.txt_2 | 1.2094800 | 1.65707 | 0.586667 |
| parent_unlinked_2_summary.txt_3 | 1.2352000 | 1.65618 | 0.903846 |
| parent_unlinked_2_summary.txt_4 | 1.2041800 | 1.67285 | 0.753846 |
| parent_unlinked_3_summary.txt_1 | 1.2478800 | 1.57238 | 1.000000 |
| parent_unlinked_3_summary.txt_2 | 1.2094800 | 1.65707 | 0.586667 |
| parent_unlinked_3_summary.txt_3 | 1.2352000 | 1.65618 | 0.903846 |
| parent_unlinked_3_summary.txt_4 | 1.2041800 | 1.67285 | 0.753846 |
| parent_unlinked_4_summary.txt_1 | 0.0426554 | 1.58862 | 0.779661 |
| parent_unlinked_4_summary.txt_2 | 0.0423615 | 1.66887 | 1.066670 |
| parent_unlinked_4_summary.txt_3 | 0.0420778 | 1.76386 | 1.114750 |
| parent_unlinked_4_summary.txt_4 | 0.0413643 | 1.75878 | 0.666667 |
| parent_unlinked_5_summary.txt_1 | 0.0426554 | 1.58862 | 0.779661 |
| parent_unlinked_5_summary.txt_2 | 0.0423615 | 1.66887 | 1.066670 |
| parent_unlinked_5_summary.txt_3 | 0.0420778 | 1.76386 | 1.114750 |
| parent_unlinked_5_summary.txt_4 | 0.0413643 | 1.75878 | 0.666667 |
Variation was maintained in 20 of the 20. 0 of the 20 populations crashed. Of the 20 replicates, 20 reached an equilibrium by 10000 generations.
Let’s take a look at how the parent trait values evolve
Evolution of parenting trait values with additive genetic variation
Frequency of parent morph with unlinked loci without viability selection (each color represents a different replicate)
Again, inference is facilitated by looking at the final frequencies and fitnesses in each replicate:
| ParentFreq | ParentW | NonParentW | |
|---|---|---|---|
| parent_unlinked_novs_1_summary.txt_1 | 0.821429 | 1.68798 | 0.729412 |
| parent_unlinked_novs_1_summary.txt_2 | 0.897030 | 1.58278 | 1.019230 |
| parent_unlinked_novs_1_summary.txt_3 | 0.897287 | 1.65443 | 0.886792 |
| parent_unlinked_novs_1_summary.txt_4 | 0.889571 | 1.67126 | 0.666667 |
| parent_unlinked_novs_2_summary.txt_1 | 0.821429 | 1.68798 | 0.729412 |
| parent_unlinked_novs_2_summary.txt_2 | 0.897030 | 1.58278 | 1.019230 |
| parent_unlinked_novs_2_summary.txt_3 | 0.897287 | 1.65443 | 0.886792 |
| parent_unlinked_novs_2_summary.txt_4 | 0.889571 | 1.67126 | 0.666667 |
| parent_unlinked_novs_3_summary.txt_1 | 0.821429 | 1.68798 | 0.729412 |
| parent_unlinked_novs_3_summary.txt_2 | 0.897030 | 1.58278 | 1.019230 |
| parent_unlinked_novs_3_summary.txt_3 | 0.897287 | 1.65443 | 0.886792 |
| parent_unlinked_novs_3_summary.txt_4 | 0.889571 | 1.67126 | 0.666667 |
| parent_unlinked_novs_4_summary.txt_1 | 0.878431 | 1.70089 | 0.709677 |
| parent_unlinked_novs_4_summary.txt_2 | 0.876797 | 1.70726 | 0.616667 |
| parent_unlinked_novs_4_summary.txt_3 | 0.855131 | 1.66824 | 0.513889 |
| parent_unlinked_novs_4_summary.txt_4 | 0.859961 | 1.61239 | 0.422535 |
| parent_unlinked_novs_5_summary.txt_1 | 0.878431 | 1.70089 | 0.709677 |
| parent_unlinked_novs_5_summary.txt_2 | 0.876797 | 1.70726 | 0.616667 |
| parent_unlinked_novs_5_summary.txt_3 | 0.855131 | 1.66824 | 0.513889 |
| parent_unlinked_novs_5_summary.txt_4 | 0.859961 | 1.61239 | 0.422535 |
Variation was maintained in 20 of the 20. 0 of the 20 populations crashed. Of the 20 replicates, 20 reached an equilibrium by 10000 generations.
Let’s take a look at how the parent trait values evolve
Evolution of parenting trait values with additive genetic variation and no viability selection
Females choose nests based on males’ courtship trait (they all only nest with courting males, and the female preference does not have a genetic basis and does not evolve), and then the survival of the nest depends on whether the courting male is also a parental male. If the chosen male is a parental male, the nest has a 90% chance of survival. Otherwise, it only has a 10% chance. Non-courters and non-parents can reproduce through sneaking.
The different runs have different outcomes.
Let’s look at the morph frequencies for each run.
Frequency of the 4 morphs in each rep with unlinked genetic variation
In some of the runs the population crashed after few generations. This is obvious when looking at the the final frequencies in a table as well:
| Generation | Pop | PopSize | NumMal | NumFem | NumProgeny | ParentThresh | ParentAEmean | ParentAEsd | ParentFreq | ParentW | NonParentW | CourterThresh | CourterAEmean | CourterAEsd | CourterFreq | CourterW | NonCourterW | FreqNcNp | FreqCNp | FreqNcP | FreqCP | PrefThresh | PrefFreq | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| parent-courter_unlinked_1_summary.txt_1 | 11999 | Pop0 | 940 | 471 | 469 | 1000 | 0.890749 | 0.443737 | 0.883452 | 0.0739653 | 0.000000 | 0.362595 | -0.942183 | -0.832353 | 1.113290 | 0.556263 | 0.362595 | 0 | 0 | 0.556263 | 0.443737 | 0.000000 | NA | NA |
| parent-courter_unlinked_1_summary.txt_2 | 11999 | Pop1 | 860 | 433 | 427 | 968 | 0.890749 | 0.441109 | 0.883265 | 0.0738648 | 0.000000 | 0.545455 | -0.942183 | -0.829546 | 1.111780 | 0.558891 | 0.545455 | 0 | 0 | 0.558891 | 0.441109 | 0.000000 | NA | NA |
| parent-courter_unlinked_1_summary.txt_3 | 11999 | Pop2 | 936 | 473 | 463 | 1000 | 0.890749 | 0.437632 | 0.881182 | 0.0748110 | 0.000000 | 0.368421 | -0.942183 | -0.798195 | 1.126020 | 0.562368 | 0.368421 | 0 | 0 | 0.562368 | 0.437632 | 0.000000 | NA | NA |
| parent-courter_unlinked_1_summary.txt_4 | 11999 | Pop3 | 942 | 477 | 465 | 1000 | 0.890749 | 0.442348 | 0.881219 | 0.0751622 | 0.000000 | 0.394737 | -0.942183 | -0.798750 | 1.131310 | 0.557652 | 0.394737 | 0 | 0 | 0.557652 | 0.442348 | 0.000000 | NA | NA |
| parent-courter_unlinked_2_summary.txt_1 | 11999 | Pop0 | 940 | 471 | 469 | 1000 | 0.890749 | 0.443737 | 0.883452 | 0.0739653 | 0.000000 | 0.362595 | -0.942183 | -0.832353 | 1.113290 | 0.556263 | 0.362595 | 0 | 0 | 0.556263 | 0.443737 | 0.000000 | NA | NA |
| parent-courter_unlinked_2_summary.txt_2 | 11999 | Pop1 | 860 | 433 | 427 | 968 | 0.890749 | 0.441109 | 0.883265 | 0.0738648 | 0.000000 | 0.545455 | -0.942183 | -0.829546 | 1.111780 | 0.558891 | 0.545455 | 0 | 0 | 0.558891 | 0.441109 | 0.000000 | NA | NA |
| parent-courter_unlinked_2_summary.txt_3 | 11999 | Pop2 | 936 | 473 | 463 | 1000 | 0.890749 | 0.437632 | 0.881182 | 0.0748110 | 0.000000 | 0.368421 | -0.942183 | -0.798195 | 1.126020 | 0.562368 | 0.368421 | 0 | 0 | 0.562368 | 0.437632 | 0.000000 | NA | NA |
| parent-courter_unlinked_2_summary.txt_4 | 11999 | Pop3 | 942 | 477 | 465 | 1000 | 0.890749 | 0.442348 | 0.881219 | 0.0751622 | 0.000000 | 0.394737 | -0.942183 | -0.798750 | 1.131310 | 0.557652 | 0.394737 | 0 | 0 | 0.557652 | 0.442348 | 0.000000 | NA | NA |
| parent-courter_unlinked_3_summary.txt_1 | 11999 | Pop0 | 940 | 471 | 469 | 1000 | 0.890749 | 0.443737 | 0.883452 | 0.0739653 | 0.000000 | 0.362595 | -0.942183 | -0.832353 | 1.113290 | 0.556263 | 0.362595 | 0 | 0 | 0.556263 | 0.443737 | 0.000000 | NA | NA |
| parent-courter_unlinked_3_summary.txt_2 | 11999 | Pop1 | 860 | 433 | 427 | 968 | 0.890749 | 0.441109 | 0.883265 | 0.0738648 | 0.000000 | 0.545455 | -0.942183 | -0.829546 | 1.111780 | 0.558891 | 0.545455 | 0 | 0 | 0.558891 | 0.441109 | 0.000000 | NA | NA |
| parent-courter_unlinked_3_summary.txt_3 | 11999 | Pop2 | 936 | 473 | 463 | 1000 | 0.890749 | 0.437632 | 0.881182 | 0.0748110 | 0.000000 | 0.368421 | -0.942183 | -0.798195 | 1.126020 | 0.562368 | 0.368421 | 0 | 0 | 0.562368 | 0.437632 | 0.000000 | NA | NA |
| parent-courter_unlinked_3_summary.txt_4 | 11999 | Pop3 | 942 | 477 | 465 | 1000 | 0.890749 | 0.442348 | 0.881219 | 0.0751622 | 0.000000 | 0.394737 | -0.942183 | -0.798750 | 1.131310 | 0.557652 | 0.394737 | 0 | 0 | 0.557652 | 0.442348 | 0.000000 | NA | NA |
| parent-courter_unlinked_4_summary.txt_1 | 11999 | Pop0 | 964 | 465 | 499 | 1000 | -0.536111 | 0.565591 | -0.587407 | 0.3684840 | 1.022810 | 0.391089 | -0.690850 | -0.600370 | 0.649948 | 0.686022 | 1.090910 | 0 | 0 | 0.434409 | 0.313978 | 0.251613 | NA | NA |
| parent-courter_unlinked_4_summary.txt_2 | 11999 | Pop1 | 962 | 479 | 483 | 1000 | -0.536111 | 0.544885 | -0.583240 | 0.3808790 | 0.762452 | 0.435780 | -0.690850 | -0.607720 | 0.671811 | 0.655532 | 0.936306 | 0 | 0 | 0.455115 | 0.344468 | 0.200418 | NA | NA |
| parent-courter_unlinked_4_summary.txt_3 | 11999 | Pop2 | 960 | 473 | 487 | 1000 | -0.536111 | 0.532770 | -0.594644 | 0.3802730 | 0.777778 | 0.384615 | -0.690850 | -0.587605 | 0.670742 | 0.670190 | 0.886435 | 0 | 0 | 0.467230 | 0.329810 | 0.202960 | NA | NA |
| parent-courter_unlinked_4_summary.txt_4 | 11999 | Pop3 | 958 | 479 | 479 | 1000 | -0.536111 | 0.582463 | -0.564566 | 0.3733460 | 0.946237 | 0.305000 | -0.690850 | -0.640658 | 0.658524 | 0.649269 | 1.045020 | 0 | 0 | 0.417537 | 0.350731 | 0.231733 | NA | NA |
| parent-courter_unlinked_5_summary.txt_1 | 11999 | Pop0 | 964 | 465 | 499 | 1000 | -0.536111 | 0.565591 | -0.587407 | 0.3684840 | 1.022810 | 0.391089 | -0.690850 | -0.600370 | 0.649948 | 0.686022 | 1.090910 | 0 | 0 | 0.434409 | 0.313978 | 0.251613 | NA | NA |
| parent-courter_unlinked_5_summary.txt_2 | 11999 | Pop1 | 962 | 479 | 483 | 1000 | -0.536111 | 0.544885 | -0.583240 | 0.3808790 | 0.762452 | 0.435780 | -0.690850 | -0.607720 | 0.671811 | 0.655532 | 0.936306 | 0 | 0 | 0.455115 | 0.344468 | 0.200418 | NA | NA |
| parent-courter_unlinked_5_summary.txt_3 | 11999 | Pop2 | 960 | 473 | 487 | 1000 | -0.536111 | 0.532770 | -0.594644 | 0.3802730 | 0.777778 | 0.384615 | -0.690850 | -0.587605 | 0.670742 | 0.670190 | 0.886435 | 0 | 0 | 0.467230 | 0.329810 | 0.202960 | NA | NA |
| parent-courter_unlinked_5_summary.txt_4 | 11999 | Pop3 | 958 | 479 | 479 | 1000 | -0.536111 | 0.582463 | -0.564566 | 0.3733460 | 0.946237 | 0.305000 | -0.690850 | -0.640658 | 0.658524 | 0.649269 | 1.045020 | 0 | 0 | 0.417537 | 0.350731 | 0.231733 | NA | NA |
Multiple morphs are maintained in 0 of the 20 replicates, and those morphs contain either a parent or a courter.
Evolution of the courter and parenting trait values in each rep with unlinked genetic variation
The different runs have different outcomes.
Let’s look at the morph frequencies for each run.
Frequency of the 4 morphs in each rep with unlinked genetic variation and no viability selection
In some of the runs the population crashed after few generations. This is obvious when looking at the the final frequencies in a table as well:
| Generation | Pop | PopSize | NumMal | NumFem | NumProgeny | ParentThresh | ParentFreq | ParentAEmean | ParentAEsd | ParentW | NonParentW | CourterThresh | CourterFreq | CourterAEmean | CourterAEsd | CourterW | NonCourterW | FreqNcNp | FreqCNp | FreqNcP | FreqCP | PrefThresh | PrefFreq | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| parent-courter_unlinked_novs_1_summary.txt_1 | 11999 | Pop0 | 966 | 504 | 462 | 1000 | 0.876646 | 0.906746 | 1.09688 | 0.235547 | 1.82276 | 1.425530 | 1.270200 | 0.906746 | 2.002970 | 0.783700 | 1.822760 | 1.42553 | 0.0932540 | 0.000000 | 0.000000 | 0.906746 | NA | NA |
| parent-courter_unlinked_novs_1_summary.txt_2 | 11999 | Pop1 | 951 | 504 | 447 | 1000 | 0.876646 | 0.898810 | 1.09639 | 0.233716 | 1.81678 | 1.470590 | 1.270200 | 0.898810 | 2.001320 | 0.777608 | 1.816780 | 1.47059 | 0.1011900 | 0.000000 | 0.000000 | 0.898810 | NA | NA |
| parent-courter_unlinked_novs_1_summary.txt_3 | 11999 | Pop2 | 949 | 472 | 477 | 1000 | 0.876646 | 0.930085 | 1.10464 | 0.237480 | 1.87699 | 1.757580 | 1.270200 | 0.930085 | 2.028780 | 0.790132 | 1.876990 | 1.75758 | 0.0699153 | 0.000000 | 0.000000 | 0.930085 | NA | NA |
| parent-courter_unlinked_novs_1_summary.txt_4 | 11999 | Pop3 | 950 | 479 | 471 | 1000 | 0.876646 | 0.908142 | 1.09918 | 0.234665 | 1.92414 | 1.431820 | 1.270200 | 0.908142 | 2.010620 | 0.780766 | 1.924140 | 1.43182 | 0.0918580 | 0.000000 | 0.000000 | 0.908142 | NA | NA |
| parent-courter_unlinked_novs_2_summary.txt_1 | 11999 | Pop0 | 966 | 504 | 462 | 1000 | 0.876646 | 0.906746 | 1.09688 | 0.235547 | 1.82276 | 1.425530 | 1.270200 | 0.906746 | 2.002970 | 0.783700 | 1.822760 | 1.42553 | 0.0932540 | 0.000000 | 0.000000 | 0.906746 | NA | NA |
| parent-courter_unlinked_novs_2_summary.txt_2 | 11999 | Pop1 | 951 | 504 | 447 | 1000 | 0.876646 | 0.898810 | 1.09639 | 0.233716 | 1.81678 | 1.470590 | 1.270200 | 0.898810 | 2.001320 | 0.777608 | 1.816780 | 1.47059 | 0.1011900 | 0.000000 | 0.000000 | 0.898810 | NA | NA |
| parent-courter_unlinked_novs_2_summary.txt_3 | 11999 | Pop2 | 949 | 472 | 477 | 1000 | 0.876646 | 0.930085 | 1.10464 | 0.237480 | 1.87699 | 1.757580 | 1.270200 | 0.930085 | 2.028780 | 0.790132 | 1.876990 | 1.75758 | 0.0699153 | 0.000000 | 0.000000 | 0.930085 | NA | NA |
| parent-courter_unlinked_novs_2_summary.txt_4 | 11999 | Pop3 | 950 | 479 | 471 | 1000 | 0.876646 | 0.908142 | 1.09918 | 0.234665 | 1.92414 | 1.431820 | 1.270200 | 0.908142 | 2.010620 | 0.780766 | 1.924140 | 1.43182 | 0.0918580 | 0.000000 | 0.000000 | 0.908142 | NA | NA |
| parent-courter_unlinked_novs_3_summary.txt_1 | 11999 | Pop0 | 966 | 504 | 462 | 1000 | 0.876646 | 0.906746 | 1.09688 | 0.235547 | 1.82276 | 1.425530 | 1.270200 | 0.906746 | 2.002970 | 0.783700 | 1.822760 | 1.42553 | 0.0932540 | 0.000000 | 0.000000 | 0.906746 | NA | NA |
| parent-courter_unlinked_novs_3_summary.txt_2 | 11999 | Pop1 | 951 | 504 | 447 | 1000 | 0.876646 | 0.898810 | 1.09639 | 0.233716 | 1.81678 | 1.470590 | 1.270200 | 0.898810 | 2.001320 | 0.777608 | 1.816780 | 1.47059 | 0.1011900 | 0.000000 | 0.000000 | 0.898810 | NA | NA |
| parent-courter_unlinked_novs_3_summary.txt_3 | 11999 | Pop2 | 949 | 472 | 477 | 1000 | 0.876646 | 0.930085 | 1.10464 | 0.237480 | 1.87699 | 1.757580 | 1.270200 | 0.930085 | 2.028780 | 0.790132 | 1.876990 | 1.75758 | 0.0699153 | 0.000000 | 0.000000 | 0.930085 | NA | NA |
| parent-courter_unlinked_novs_3_summary.txt_4 | 11999 | Pop3 | 950 | 479 | 471 | 1000 | 0.876646 | 0.908142 | 1.09918 | 0.234665 | 1.92414 | 1.431820 | 1.270200 | 0.908142 | 2.010620 | 0.780766 | 1.924140 | 1.43182 | 0.0918580 | 0.000000 | 0.000000 | 0.908142 | NA | NA |
| parent-courter_unlinked_novs_4_summary.txt_1 | 11999 | Pop0 | 1000 | 514 | 486 | 1000 | 1.188380 | 0.461089 | 1.07559 | 1.222950 | 0.00000 | 0.339350 | 0.344879 | 0.538911 | 0.373095 | 0.305945 | 0.339350 | 0.00000 | 0.0000000 | 0.538911 | 0.461089 | 0.000000 | NA | NA |
| parent-courter_unlinked_novs_4_summary.txt_2 | 11999 | Pop1 | 1000 | 519 | 481 | 1000 | 1.188380 | 0.452794 | 1.07010 | 1.230870 | 0.00000 | 0.390845 | 0.344879 | 0.547206 | 0.374467 | 0.307926 | 0.390845 | 0.00000 | 0.0000000 | 0.547206 | 0.452794 | 0.000000 | NA | NA |
| parent-courter_unlinked_novs_4_summary.txt_3 | 11999 | Pop2 | 1000 | 533 | 467 | 1000 | 1.188380 | 0.465291 | 1.07074 | 1.214330 | 0.00000 | 0.403509 | 0.344879 | 0.534709 | 0.374307 | 0.303788 | 0.403509 | 0.00000 | 0.0000000 | 0.534709 | 0.465291 | 0.000000 | NA | NA |
| parent-courter_unlinked_novs_4_summary.txt_4 | 11999 | Pop3 | 1000 | 514 | 486 | 1000 | 1.188380 | 0.463035 | 1.09061 | 1.229310 | 0.00000 | 0.489130 | 0.344879 | 0.536965 | 0.369337 | 0.307536 | 0.489130 | 0.00000 | 0.0000000 | 0.536965 | 0.463035 | 0.000000 | NA | NA |
| parent-courter_unlinked_novs_5_summary.txt_1 | 11999 | Pop0 | 1000 | 514 | 486 | 1000 | 1.188380 | 0.461089 | 1.07559 | 1.222950 | 0.00000 | 0.339350 | 0.344879 | 0.538911 | 0.373095 | 0.305945 | 0.339350 | 0.00000 | 0.0000000 | 0.538911 | 0.461089 | 0.000000 | NA | NA |
| parent-courter_unlinked_novs_5_summary.txt_2 | 11999 | Pop1 | 1000 | 519 | 481 | 1000 | 1.188380 | 0.452794 | 1.07010 | 1.230870 | 0.00000 | 0.390845 | 0.344879 | 0.547206 | 0.374467 | 0.307926 | 0.390845 | 0.00000 | 0.0000000 | 0.547206 | 0.452794 | 0.000000 | NA | NA |
| parent-courter_unlinked_novs_5_summary.txt_3 | 11999 | Pop2 | 1000 | 533 | 467 | 1000 | 1.188380 | 0.465291 | 1.07074 | 1.214330 | 0.00000 | 0.403509 | 0.344879 | 0.534709 | 0.374307 | 0.303788 | 0.403509 | 0.00000 | 0.0000000 | 0.534709 | 0.465291 | 0.000000 | NA | NA |
| parent-courter_unlinked_novs_5_summary.txt_4 | 11999 | Pop3 | 1000 | 514 | 486 | 1000 | 1.188380 | 0.463035 | 1.09061 | 1.229310 | 0.00000 | 0.489130 | 0.344879 | 0.536965 | 0.369337 | 0.307536 | 0.489130 | 0.00000 | 0.0000000 | 0.536965 | 0.463035 | 0.000000 | NA | NA |
Multiple morphs are maintained in 20 of the 20 replicates, and those morphs contain either a parent or a courter.
Evolution of the courter and parenting trait values in each rep with unlinked genetic variation and without viability selection
In these cases, the traits are encoded by a number (50) of loci, whose alleles contribute additively to determine the trait value. These alleles anchored on chromosomes, equally distributed among the chromosomes (4). The overall trait value is compared to a population-level threshold (which is static, in these cases), and if the trait value is above the threshold the male takes the parent or courter morph and if it is below he does not. Below, I’m showing the results from 10 replicates of each scenario.
Frequency of the courter morph with linked QTLs (each color represents a different replicate)
When only the courtship trait is included in the simulation, 0 of the 20 replicates reached an equilibrium by 10000 generations.
This is further evidenced by looking at a table of trait values and fitnesses in the final generation of each replicate
| CourterFreq | CourterW | NonCourterW | |
|---|---|---|---|
| courter_linked_1_summary.txt_1 | 1 | 1.99800 | 0 |
| courter_linked_1_summary.txt_2 | 1 | 2.02439 | 0 |
| courter_linked_1_summary.txt_3 | 1 | 1.96457 | 0 |
| courter_linked_1_summary.txt_4 | 1 | 2.02028 | 0 |
| courter_linked_2_summary.txt_1 | 1 | 1.92070 | 0 |
| courter_linked_2_summary.txt_2 | 1 | 2.05350 | 0 |
| courter_linked_2_summary.txt_3 | 1 | 2.00605 | 0 |
| courter_linked_2_summary.txt_4 | 1 | 2.01826 | 0 |
| courter_linked_3_summary.txt_1 | 1 | 1.99800 | 0 |
| courter_linked_3_summary.txt_2 | 1 | 2.02439 | 0 |
| courter_linked_3_summary.txt_3 | 1 | 1.96457 | 0 |
| courter_linked_3_summary.txt_4 | 1 | 2.02028 | 0 |
| courter_linked_4_summary.txt_1 | 1 | 2.00000 | 0 |
| courter_linked_4_summary.txt_2 | 1 | 2.00401 | 0 |
| courter_linked_4_summary.txt_3 | 1 | 2.02020 | 0 |
| courter_linked_4_summary.txt_4 | 1 | 1.94175 | 0 |
| courter_linked_5_summary.txt_1 | 1 | 2.00000 | 0 |
| courter_linked_5_summary.txt_2 | 1 | 2.00401 | 0 |
| courter_linked_5_summary.txt_3 | 1 | 2.02020 | 0 |
| courter_linked_5_summary.txt_4 | 1 | 1.94175 | 0 |
Every rep has the courtship trait go to fixation.
Let’s also evaluate the evolution of the courtship trait values:
Evolution of courtship trait with linked loci
Frequency of the courter morph with linked QTLs and no viability selection (each color represents a different replicate)
When only the courtship trait is included in the simulation, 0 of the 20 replicates reached an equilibrium by 10000 generations.
This is further evidenced by looking at a table of trait values and fitnesses in the final generation of each replicate
| CourterFreq | CourterW | NonCourterW | |
|---|---|---|---|
| courter_linked_novs_1_summary.txt_1 | 1 | 1.99203 | 0 |
| courter_linked_novs_1_summary.txt_2 | 1 | 1.95312 | 0 |
| courter_linked_novs_1_summary.txt_3 | 1 | 2.03666 | 0 |
| courter_linked_novs_1_summary.txt_4 | 1 | 1.96850 | 0 |
| courter_linked_novs_2_summary.txt_1 | 1 | 2.04082 | 0 |
| courter_linked_novs_2_summary.txt_2 | 1 | 2.04499 | 0 |
| courter_linked_novs_2_summary.txt_3 | 1 | 2.05339 | 0 |
| courter_linked_novs_2_summary.txt_4 | 1 | 1.92308 | 0 |
| courter_linked_novs_3_summary.txt_1 | 1 | 1.99203 | 0 |
| courter_linked_novs_3_summary.txt_2 | 1 | 1.95312 | 0 |
| courter_linked_novs_3_summary.txt_3 | 1 | 2.03666 | 0 |
| courter_linked_novs_3_summary.txt_4 | 1 | 1.96850 | 0 |
| courter_linked_novs_4_summary.txt_1 | 1 | 1.94175 | 0 |
| courter_linked_novs_4_summary.txt_2 | 1 | 2.02020 | 0 |
| courter_linked_novs_4_summary.txt_3 | 1 | 2.05339 | 0 |
| courter_linked_novs_4_summary.txt_4 | 1 | 1.97239 | 0 |
| courter_linked_novs_5_summary.txt_1 | 1 | 1.94175 | 0 |
| courter_linked_novs_5_summary.txt_2 | 1 | 2.02020 | 0 |
| courter_linked_novs_5_summary.txt_3 | 1 | 2.05339 | 0 |
| courter_linked_novs_5_summary.txt_4 | 1 | 1.97239 | 0 |
Every rep has the courtship trait go to fixation.
Let’s also evaluate the evolution of the courtship trait values:
Evolution of courtship trait with linked loci and without viability selection
Frequency of parent morph with linked QTLs (each color represents a different replicate)
When only the parental trait is included in the model with linked QTLs, variable outcomes can be reached – although all include each rep reaching some stable state with minor fluctuations.
| ParentFreq | ParentW | NonParentW | |
|---|---|---|---|
| parent_linked_1_summary.txt_1 | 0.600465 | 1.54780 | 0.443478 |
| parent_linked_1_summary.txt_2 | 0.547665 | 1.64390 | 0.390805 |
| parent_linked_1_summary.txt_3 | 0.526249 | 1.41768 | 0.302703 |
| parent_linked_1_summary.txt_4 | 0.574138 | 1.57957 | 0.681319 |
| parent_linked_2_summary.txt_1 | 0.600465 | 1.54780 | 0.443478 |
| parent_linked_2_summary.txt_2 | 0.547665 | 1.64390 | 0.390805 |
| parent_linked_2_summary.txt_3 | 0.526249 | 1.41768 | 0.302703 |
| parent_linked_2_summary.txt_4 | 0.574138 | 1.57957 | 0.681319 |
| parent_linked_3_summary.txt_1 | 0.589370 | 1.55238 | 0.424242 |
| parent_linked_3_summary.txt_2 | 0.580436 | 1.45682 | 0.464286 |
| parent_linked_3_summary.txt_3 | 0.579465 | 1.68905 | 0.525773 |
| parent_linked_3_summary.txt_4 | 0.591772 | 1.50962 | 0.752577 |
| parent_linked_4_summary.txt_1 | 0.240375 | 1.55125 | 0.710145 |
| parent_linked_4_summary.txt_2 | 0.231262 | 1.73861 | 0.446429 |
| parent_linked_4_summary.txt_3 | 0.234927 | 1.60766 | 0.734940 |
| parent_linked_4_summary.txt_4 | 0.236218 | 1.57267 | 1.017240 |
| parent_linked_5_summary.txt_1 | 0.240375 | 1.55125 | 0.710145 |
| parent_linked_5_summary.txt_2 | 0.231262 | 1.73861 | 0.446429 |
| parent_linked_5_summary.txt_3 | 0.234927 | 1.60766 | 0.734940 |
| parent_linked_5_summary.txt_4 | 0.236218 | 1.57267 | 1.017240 |
Variation was maintained in 20 of the 20. 0 of the 20 populations crashed. Of the 20 replicates, 20 reached an equilibrium by 10000 generations.
The evolution of the trait values may shed light on the variable outcomes:
Evolution of parenting trait values with linked QTLs
Frequency of parent morph with linked QTLs without viability selection (each color represents a different replicate)
When only the parental trait is included in the model with linked QTLs, variable outcomes can be reached – although all include each rep reaching some stable state with minor fluctuations.
| ParentFreq | ParentW | NonParentW | |
|---|---|---|---|
| parent_linked_novs_1_summary.txt_1 | 0.825581 | 1.61737 | 0.511111 |
| parent_linked_novs_1_summary.txt_2 | 0.606000 | 1.62706 | 0.324873 |
| parent_linked_novs_1_summary.txt_3 | 0.736196 | 1.65000 | 0.496124 |
| parent_linked_novs_1_summary.txt_4 | 0.795082 | 1.60052 | 0.510000 |
| parent_linked_novs_2_summary.txt_1 | 0.715768 | 1.72754 | 0.386861 |
| parent_linked_novs_2_summary.txt_2 | 0.834264 | 1.51562 | 0.561798 |
| parent_linked_novs_2_summary.txt_3 | 0.684803 | 1.57260 | 0.488095 |
| parent_linked_novs_2_summary.txt_4 | 0.817269 | 1.55774 | 0.703297 |
| parent_linked_novs_3_summary.txt_1 | 0.715768 | 1.72754 | 0.386861 |
| parent_linked_novs_3_summary.txt_2 | 0.834264 | 1.51562 | 0.561798 |
| parent_linked_novs_3_summary.txt_3 | 0.684803 | 1.57260 | 0.488095 |
| parent_linked_novs_3_summary.txt_4 | 0.817269 | 1.55774 | 0.703297 |
| parent_linked_novs_4_summary.txt_1 | 0.745902 | 1.59615 | 0.612903 |
| parent_linked_novs_4_summary.txt_2 | 0.781250 | 1.71500 | 0.482143 |
| parent_linked_novs_4_summary.txt_3 | 0.814453 | 1.50600 | 0.631579 |
| parent_linked_novs_4_summary.txt_4 | 0.782435 | 1.61735 | 0.513761 |
| parent_linked_novs_5_summary.txt_1 | 0.745902 | 1.59615 | 0.612903 |
| parent_linked_novs_5_summary.txt_2 | 0.781250 | 1.71500 | 0.482143 |
| parent_linked_novs_5_summary.txt_3 | 0.814453 | 1.50600 | 0.631579 |
| parent_linked_novs_5_summary.txt_4 | 0.782435 | 1.61735 | 0.513761 |
Variation was maintained in 20 of the 20. 0 of the 20 populations crashed. Of the 20 replicates, 20 reached an equilibrium by 10000 generations.
The evolution of the trait values may shed light on the variable outcomes:
Evolution of parenting trait values with linked QTLs and without viability selection
Including both courtship and parental traits, along with linked loci, causes the outcomes to be even less predictable.
Frequency of the two morphs with linked QTLs (courter = green, parent = blue)
Because of the variable outcomes, it is useful to visualize the frequencies of the four morphs with each rep in its own graph.
Frequency of the 4 morphs in each rep with linked QTLs
In some of the runs the population crashed after few generations. This is obvious both from the figures and when looking at the the final frequencies in a table as well (pay attention to the generation number column):
| Generation | Pop | PopSize | NumMal | NumFem | NumProgeny | ParentThresh | ParentAEmean | ParentAEsd | ParentFreq | ParentW | NonParentW | CourterThresh | CourterAEmean | CourterAEsd | CourterFreq | CourterW | NonCourterW | FreqNcNp | FreqCNp | FreqNcP | FreqCP | PrefThresh | PrefFreq | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| parent-courter_linked_1_summary.txt_1 | 11999 | Pop0 | 1000 | 494 | 506 | 1000 | -0.458612 | 0.447368 | -0.4942660 | 0.4957500 | 0.0090498 | 0.326007 | 0.343049 | 0.376947 | 0.473095 | 0.556680 | 0.330909 | 0 | 0.0000000 | 0.552632 | 0.443320 | 0.0040486 | NA | NA |
| parent-courter_linked_1_summary.txt_2 | 11999 | Pop1 | 998 | 507 | 491 | 1000 | -0.458612 | 0.439842 | -0.5044700 | 0.4945260 | 0.0000000 | 0.299296 | 0.343049 | 0.386529 | 0.471814 | 0.560158 | 0.299296 | 0 | 0.0000000 | 0.560158 | 0.439842 | 0.0000000 | NA | NA |
| parent-courter_linked_1_summary.txt_3 | 11999 | Pop2 | 1000 | 508 | 492 | 1000 | -0.458612 | 0.442913 | -0.5021480 | 0.4959020 | 0.0000000 | 0.314488 | 0.343049 | 0.384785 | 0.473144 | 0.557087 | 0.314488 | 0 | 0.0000000 | 0.557087 | 0.442913 | 0.0000000 | NA | NA |
| parent-courter_linked_1_summary.txt_4 | 11999 | Pop3 | 1000 | 484 | 516 | 1000 | -0.458612 | 0.440083 | -0.4950940 | 0.5009730 | 0.0000000 | 0.479705 | 0.343049 | 0.378210 | 0.478414 | 0.559917 | 0.479705 | 0 | 0.0000000 | 0.559917 | 0.440083 | 0.0000000 | NA | NA |
| parent-courter_linked_2_summary.txt_1 | 11999 | Pop0 | 1000 | 494 | 506 | 1000 | -0.458612 | 0.447368 | -0.4942660 | 0.4957500 | 0.0090498 | 0.326007 | 0.343049 | 0.376947 | 0.473095 | 0.556680 | 0.330909 | 0 | 0.0000000 | 0.552632 | 0.443320 | 0.0040486 | NA | NA |
| parent-courter_linked_2_summary.txt_2 | 11999 | Pop1 | 998 | 507 | 491 | 1000 | -0.458612 | 0.439842 | -0.5044700 | 0.4945260 | 0.0000000 | 0.299296 | 0.343049 | 0.386529 | 0.471814 | 0.560158 | 0.299296 | 0 | 0.0000000 | 0.560158 | 0.439842 | 0.0000000 | NA | NA |
| parent-courter_linked_2_summary.txt_3 | 11999 | Pop2 | 1000 | 508 | 492 | 1000 | -0.458612 | 0.442913 | -0.5021480 | 0.4959020 | 0.0000000 | 0.314488 | 0.343049 | 0.384785 | 0.473144 | 0.557087 | 0.314488 | 0 | 0.0000000 | 0.557087 | 0.442913 | 0.0000000 | NA | NA |
| parent-courter_linked_2_summary.txt_4 | 11999 | Pop3 | 1000 | 484 | 516 | 1000 | -0.458612 | 0.440083 | -0.4950940 | 0.5009730 | 0.0000000 | 0.479705 | 0.343049 | 0.378210 | 0.478414 | 0.559917 | 0.479705 | 0 | 0.0000000 | 0.559917 | 0.440083 | 0.0000000 | NA | NA |
| parent-courter_linked_3_summary.txt_1 | 11999 | Pop0 | 1000 | 494 | 506 | 1000 | -0.458612 | 0.447368 | -0.4942660 | 0.4957500 | 0.0090498 | 0.326007 | 0.343049 | 0.376947 | 0.473095 | 0.556680 | 0.330909 | 0 | 0.0000000 | 0.552632 | 0.443320 | 0.0040486 | NA | NA |
| parent-courter_linked_3_summary.txt_2 | 11999 | Pop1 | 998 | 507 | 491 | 1000 | -0.458612 | 0.439842 | -0.5044700 | 0.4945260 | 0.0000000 | 0.299296 | 0.343049 | 0.386529 | 0.471814 | 0.560158 | 0.299296 | 0 | 0.0000000 | 0.560158 | 0.439842 | 0.0000000 | NA | NA |
| parent-courter_linked_3_summary.txt_3 | 11999 | Pop2 | 1000 | 508 | 492 | 1000 | -0.458612 | 0.442913 | -0.5021480 | 0.4959020 | 0.0000000 | 0.314488 | 0.343049 | 0.384785 | 0.473144 | 0.557087 | 0.314488 | 0 | 0.0000000 | 0.557087 | 0.442913 | 0.0000000 | NA | NA |
| parent-courter_linked_3_summary.txt_4 | 11999 | Pop3 | 1000 | 484 | 516 | 1000 | -0.458612 | 0.440083 | -0.4950940 | 0.5009730 | 0.0000000 | 0.479705 | 0.343049 | 0.378210 | 0.478414 | 0.559917 | 0.479705 | 0 | 0.0000000 | 0.559917 | 0.440083 | 0.0000000 | NA | NA |
| parent-courter_linked_4_summary.txt_1 | 2042 | Pop0 | 147 | 69 | 78 | 209 | 0.140770 | 0.231884 | 0.1033710 | 0.0523604 | 0.0000000 | 0.509434 | -1.438140 | -1.214650 | 0.311778 | 0.768116 | 0.509434 | 0 | 0.0000000 | 0.768116 | 0.231884 | 0.0000000 | NA | NA |
| parent-courter_linked_4_summary.txt_2 | 2041 | Pop1 | 4 | 3 | 1 | 4 | 0.140770 | 0.000000 | 0.0604539 | 0.0803165 | 0.0000000 | 1.333330 | -1.438140 | -0.975535 | 0.462605 | 1.000000 | 1.333330 | 0 | 0.0000000 | 1.000000 | 0.000000 | 0.0000000 | NA | NA |
| parent-courter_linked_4_summary.txt_3 | 2041 | Pop2 | 151 | 77 | 74 | 194 | 0.140770 | 0.363636 | 0.1098850 | 0.0542629 | 0.0000000 | 0.408163 | -1.438140 | -1.260750 | 0.311511 | 0.636364 | 0.408163 | 0 | 0.0000000 | 0.636364 | 0.363636 | 0.0000000 | NA | NA |
| parent-courter_linked_4_summary.txt_4 | 2041 | Pop3 | 149 | 76 | 73 | 182 | 0.140770 | 0.421053 | 0.1260010 | 0.0376265 | 0.1250000 | 0.568182 | -1.438140 | -1.345830 | 0.215691 | 0.605263 | 0.630435 | 0 | 0.0131579 | 0.565789 | 0.381579 | 0.0394737 | NA | NA |
| parent-courter_linked_5_summary.txt_1 | 2042 | Pop0 | 147 | 69 | 78 | 209 | 0.140770 | 0.231884 | 0.1033710 | 0.0523604 | 0.0000000 | 0.509434 | -1.438140 | -1.214650 | 0.311778 | 0.768116 | 0.509434 | 0 | 0.0000000 | 0.768116 | 0.231884 | 0.0000000 | NA | NA |
| parent-courter_linked_5_summary.txt_2 | 2041 | Pop1 | 4 | 3 | 1 | 4 | 0.140770 | 0.000000 | 0.0604539 | 0.0803165 | 0.0000000 | 1.333330 | -1.438140 | -0.975535 | 0.462605 | 1.000000 | 1.333330 | 0 | 0.0000000 | 1.000000 | 0.000000 | 0.0000000 | NA | NA |
| parent-courter_linked_5_summary.txt_3 | 2041 | Pop2 | 151 | 77 | 74 | 194 | 0.140770 | 0.363636 | 0.1098850 | 0.0542629 | 0.0000000 | 0.408163 | -1.438140 | -1.260750 | 0.311511 | 0.636364 | 0.408163 | 0 | 0.0000000 | 0.636364 | 0.363636 | 0.0000000 | NA | NA |
| parent-courter_linked_5_summary.txt_4 | 2041 | Pop3 | 149 | 76 | 73 | 182 | 0.140770 | 0.421053 | 0.1260010 | 0.0376265 | 0.1250000 | 0.568182 | -1.438140 | -1.345830 | 0.215691 | 0.605263 | 0.630435 | 0 | 0.0131579 | 0.565789 | 0.381579 | 0.0394737 | NA | NA |
Multiple morphs are maintained in 0 of the 20 replicates, and those morphs contain either a parent or a courter. However, 8 of those reps with variation actually crashed.
Looking at the trait value evolution may help us understand why some of the runs resulted in extinction:
Evolution of the courter and parenting trait values in each rep with linked genetic variation
Frequency of the two morphs with linked QTLs and without viability selection (courter = green, parent = blue)
Because of the variable outcomes, it is useful to visualize the frequencies of the four morphs with each rep in its own graph.
Frequency of the 4 morphs in each rep with linked QTLs without viability selection
In some of the runs the population crashed after few generations. This is obvious both from the figures and when looking at the the final frequencies in a table as well (pay attention to the generation number column):
| Generation | Pop | PopSize | NumMal | NumFem | NumProgeny | ParentThresh | ParentFreq | ParentAEmean | ParentAEsd | ParentW | NonParentW | CourterThresh | CourterFreq | CourterAEmean | CourterAEsd | CourterW | NonCourterW | FreqNcNp | FreqCNp | FreqNcP | FreqCP | PrefThresh | PrefFreq | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| parent-courter_linked_novs_1_summary.txt_1 | 11999 | Pop0 | 1000 | 480 | 520 | 1000 | 0.933615 | 0.897917 | 1.333910 | 0.579584 | 1.9373500 | 1.306120 | -0.114728 | 0.893750 | 0.182179 | 0.4312150 | 1.967370 | 1.078430 | 0.0895833 | 0.0125000 | 0.0166667 | 0.8812500 | NA | NA |
| parent-courter_linked_novs_1_summary.txt_2 | 11999 | Pop1 | 993 | 499 | 494 | 1000 | 0.933615 | 0.885772 | 1.314860 | 0.563536 | 1.8936700 | 1.140350 | -0.114728 | 0.887776 | 0.160480 | 0.4118220 | 1.896160 | 1.107140 | 0.1042080 | 0.0100200 | 0.0080160 | 0.8777560 | NA | NA |
| parent-courter_linked_novs_1_summary.txt_3 | 11999 | Pop2 | 989 | 461 | 528 | 1000 | 0.933615 | 0.893709 | 1.335020 | 0.576297 | 2.0048500 | 1.367350 | -0.114728 | 0.908894 | 0.191017 | 0.4312860 | 1.983290 | 1.476190 | 0.0867679 | 0.0195228 | 0.0043384 | 0.8893710 | NA | NA |
| parent-courter_linked_novs_1_summary.txt_4 | 11999 | Pop3 | 993 | 513 | 480 | 1000 | 0.933615 | 0.851852 | 1.265330 | 0.522345 | 1.7597300 | 1.092110 | -0.114728 | 0.867446 | 0.137293 | 0.3860480 | 1.759550 | 1.014710 | 0.1130600 | 0.0350877 | 0.0194932 | 0.8323590 | NA | NA |
| parent-courter_linked_novs_2_summary.txt_1 | 11999 | Pop0 | 1000 | 493 | 507 | 1000 | 0.933615 | 0.920892 | 1.397390 | 0.621610 | 1.8281900 | 1.282050 | -0.114728 | 0.920892 | 0.218400 | 0.4506270 | 1.848020 | 1.051280 | 0.0669371 | 0.0121704 | 0.0121704 | 0.9087220 | NA | NA |
| parent-courter_linked_novs_2_summary.txt_2 | 11999 | Pop1 | 1000 | 526 | 474 | 1000 | 0.933615 | 0.910646 | 1.342900 | 0.567567 | 1.7411300 | 1.191490 | -0.114728 | 0.927757 | 0.215363 | 0.4381490 | 1.739750 | 1.078950 | 0.0665399 | 0.0228137 | 0.0057034 | 0.9049430 | NA | NA |
| parent-courter_linked_novs_2_summary.txt_3 | 11999 | Pop2 | 1000 | 506 | 494 | 1000 | 0.933615 | 0.899209 | 1.353970 | 0.582419 | 1.7868100 | 0.686275 | -0.114728 | 0.909091 | 0.189434 | 0.4227330 | 1.776090 | 0.673913 | 0.0849802 | 0.0158103 | 0.0059288 | 0.8932810 | NA | NA |
| parent-courter_linked_novs_2_summary.txt_4 | 11999 | Pop3 | 1000 | 467 | 533 | 1000 | 0.933615 | 0.877944 | 1.347710 | 0.617913 | 1.9902400 | 1.333330 | -0.114728 | 0.890792 | 0.179219 | 0.4437650 | 1.978370 | 1.352940 | 0.1049250 | 0.0171306 | 0.0042827 | 0.8736620 | NA | NA |
| parent-courter_linked_novs_3_summary.txt_1 | 11999 | Pop0 | 1000 | 493 | 507 | 1000 | 0.933615 | 0.920892 | 1.397390 | 0.621610 | 1.8281900 | 1.282050 | -0.114728 | 0.920892 | 0.218400 | 0.4506270 | 1.848020 | 1.051280 | 0.0669371 | 0.0121704 | 0.0121704 | 0.9087220 | NA | NA |
| parent-courter_linked_novs_3_summary.txt_2 | 11999 | Pop1 | 1000 | 526 | 474 | 1000 | 0.933615 | 0.910646 | 1.342900 | 0.567567 | 1.7411300 | 1.191490 | -0.114728 | 0.927757 | 0.215363 | 0.4381490 | 1.739750 | 1.078950 | 0.0665399 | 0.0228137 | 0.0057034 | 0.9049430 | NA | NA |
| parent-courter_linked_novs_3_summary.txt_3 | 11999 | Pop2 | 1000 | 506 | 494 | 1000 | 0.933615 | 0.899209 | 1.353970 | 0.582419 | 1.7868100 | 0.686275 | -0.114728 | 0.909091 | 0.189434 | 0.4227330 | 1.776090 | 0.673913 | 0.0849802 | 0.0158103 | 0.0059288 | 0.8932810 | NA | NA |
| parent-courter_linked_novs_3_summary.txt_4 | 11999 | Pop3 | 1000 | 467 | 533 | 1000 | 0.933615 | 0.877944 | 1.347710 | 0.617913 | 1.9902400 | 1.333330 | -0.114728 | 0.890792 | 0.179219 | 0.4437650 | 1.978370 | 1.352940 | 0.1049250 | 0.0171306 | 0.0042827 | 0.8736620 | NA | NA |
| parent-courter_linked_novs_4_summary.txt_1 | 11999 | Pop0 | 980 | 512 | 468 | 1000 | -0.105665 | 0.464844 | -0.114794 | 0.108740 | 0.0294118 | 0.412409 | -0.359170 | 0.537109 | -0.356093 | 0.0364008 | 0.436364 | 0.000000 | 0.0019531 | 0.5332030 | 0.4609380 | 0.0039062 | NA | NA |
| parent-courter_linked_novs_4_summary.txt_2 | 11999 | Pop1 | 980 | 499 | 481 | 1000 | -0.105665 | 0.464930 | -0.112029 | 0.107393 | 0.0000000 | 0.453184 | -0.359170 | 0.535070 | -0.356999 | 0.0359518 | 0.453184 | 0.000000 | 0.0000000 | 0.5350700 | 0.4649300 | 0.0000000 | NA | NA |
| parent-courter_linked_novs_4_summary.txt_3 | 11999 | Pop2 | 979 | 504 | 475 | 1000 | -0.105665 | 0.462302 | -0.114977 | 0.109187 | 0.0000000 | 0.372694 | -0.359170 | 0.535714 | -0.356055 | 0.0365506 | 0.374074 | 0.000000 | 0.0019841 | 0.5357140 | 0.4623020 | 0.0000000 | NA | NA |
| parent-courter_linked_novs_4_summary.txt_4 | 11999 | Pop3 | 983 | 515 | 468 | 1000 | -0.105665 | 0.454369 | -0.116693 | 0.108979 | 0.0000000 | 0.327402 | -0.359170 | 0.545631 | -0.355486 | 0.0364892 | 0.327402 | 0.000000 | 0.0000000 | 0.5456310 | 0.4543690 | 0.0000000 | NA | NA |
| parent-courter_linked_novs_5_summary.txt_1 | 11999 | Pop0 | 980 | 512 | 468 | 1000 | -0.105665 | 0.464844 | -0.114794 | 0.108740 | 0.0294118 | 0.412409 | -0.359170 | 0.537109 | -0.356093 | 0.0364008 | 0.436364 | 0.000000 | 0.0019531 | 0.5332030 | 0.4609380 | 0.0039062 | NA | NA |
| parent-courter_linked_novs_5_summary.txt_2 | 11999 | Pop1 | 980 | 499 | 481 | 1000 | -0.105665 | 0.464930 | -0.112029 | 0.107393 | 0.0000000 | 0.453184 | -0.359170 | 0.535070 | -0.356999 | 0.0359518 | 0.453184 | 0.000000 | 0.0000000 | 0.5350700 | 0.4649300 | 0.0000000 | NA | NA |
| parent-courter_linked_novs_5_summary.txt_3 | 11999 | Pop2 | 979 | 504 | 475 | 1000 | -0.105665 | 0.462302 | -0.114977 | 0.109187 | 0.0000000 | 0.372694 | -0.359170 | 0.535714 | -0.356055 | 0.0365506 | 0.374074 | 0.000000 | 0.0019841 | 0.5357140 | 0.4623020 | 0.0000000 | NA | NA |
| parent-courter_linked_novs_5_summary.txt_4 | 11999 | Pop3 | 983 | 515 | 468 | 1000 | -0.105665 | 0.454369 | -0.116693 | 0.108979 | 0.0000000 | 0.327402 | -0.359170 | 0.545631 | -0.355486 | 0.0364892 | 0.327402 | 0.000000 | 0.0000000 | 0.5456310 | 0.4543690 | 0.0000000 | NA | NA |
Multiple morphs are maintained in 20 of the 20 replicates, and those morphs contain either a parent or a courter. However, 0 of those reps with variation actually crashed.
Looking at the trait value evolution may help us understand why some of the runs resulted in extinction:
Evolution of the courter and parenting trait values in each rep with linked genetic variation and no viability selection
In these cases, the loci (50) are all located in one region of a chromosome, and that region has reduced recombination. As above, the overall trait value is compared to a population-level threshold (which is static, in these cases), and if the trait value is above the threshold the male takes the parent or courter morph and if it is below he does not. Below, I’m showing the results from 10 replicates of each scenario.
Frequency of the courter morph with supergenes (each color represents a different replicate)
Of the 20 replicates, 0 reached an equilibrium by 10000 generations.
| CourterFreq | CourterW | NonCourterW | |
|---|---|---|---|
| courter_supergene_1_summary.txt_1 | 1 | 1.89394 | 0 |
| courter_supergene_1_summary.txt_2 | 1 | 2.08768 | 0 |
| courter_supergene_1_summary.txt_3 | 1 | 2.03252 | 0 |
| courter_supergene_1_summary.txt_4 | 1 | 2.01613 | 0 |
| courter_supergene_2_summary.txt_1 | 1 | 1.96078 | 0 |
| courter_supergene_2_summary.txt_2 | 1 | 2.00803 | 0 |
| courter_supergene_2_summary.txt_3 | 1 | 2.03666 | 0 |
| courter_supergene_2_summary.txt_4 | 1 | 1.98807 | 0 |
| courter_supergene_3_summary.txt_1 | 1 | 1.89394 | 0 |
| courter_supergene_3_summary.txt_2 | 1 | 2.08768 | 0 |
| courter_supergene_3_summary.txt_3 | 1 | 2.03252 | 0 |
| courter_supergene_3_summary.txt_4 | 1 | 2.01613 | 0 |
| courter_supergene_4_summary.txt_1 | 1 | 2.03265 | 0 |
| courter_supergene_4_summary.txt_2 | 1 | 2.12848 | 0 |
| courter_supergene_4_summary.txt_3 | 1 | 2.04517 | 0 |
| courter_supergene_4_summary.txt_4 | 1 | 2.02240 | 0 |
| courter_supergene_5_summary.txt_1 | 1 | 2.03265 | 0 |
| courter_supergene_5_summary.txt_2 | 1 | 2.12848 | 0 |
| courter_supergene_5_summary.txt_3 | 1 | 2.04517 | 0 |
| courter_supergene_5_summary.txt_4 | 1 | 2.02240 | 0 |
Looking at the evolution of the trait values:
Evolution of courtship trait with a supergene
Frequency of the courter morph with supergenes without viability selection (each color represents a different replicate)
Of the 20 replicates, 0 reached an equilibrium by 10000 generations.
| CourterFreq | CourterW | NonCourterW | |
|---|---|---|---|
| courter_supergene_novs_1_summary.txt_1 | 1 | 2.06186 | 0 |
| courter_supergene_novs_1_summary.txt_2 | 1 | 1.94553 | 0 |
| courter_supergene_novs_1_summary.txt_3 | 1 | 1.93424 | 0 |
| courter_supergene_novs_1_summary.txt_4 | 1 | 1.99601 | 0 |
| courter_supergene_novs_2_summary.txt_1 | 1 | 2.06186 | 0 |
| courter_supergene_novs_2_summary.txt_2 | 1 | 1.94553 | 0 |
| courter_supergene_novs_2_summary.txt_3 | 1 | 1.93424 | 0 |
| courter_supergene_novs_2_summary.txt_4 | 1 | 1.99601 | 0 |
| courter_supergene_novs_3_summary.txt_1 | 1 | 1.93798 | 0 |
| courter_supergene_novs_3_summary.txt_2 | 1 | 1.98807 | 0 |
| courter_supergene_novs_3_summary.txt_3 | 1 | 1.96078 | 0 |
| courter_supergene_novs_3_summary.txt_4 | 1 | 2.00000 | 0 |
| courter_supergene_novs_4_summary.txt_1 | 1 | 2.02429 | 0 |
| courter_supergene_novs_4_summary.txt_2 | 1 | 2.07469 | 0 |
| courter_supergene_novs_4_summary.txt_3 | 1 | 2.07469 | 0 |
| courter_supergene_novs_4_summary.txt_4 | 1 | 2.04499 | 0 |
| courter_supergene_novs_5_summary.txt_1 | 1 | 2.02429 | 0 |
| courter_supergene_novs_5_summary.txt_2 | 1 | 2.07469 | 0 |
| courter_supergene_novs_5_summary.txt_3 | 1 | 2.07469 | 0 |
| courter_supergene_novs_5_summary.txt_4 | 1 | 2.04499 | 0 |
Looking at the evolution of the trait values:
Evolution of courtship trait with a supergene and without viability selection
Frequency of parent morph with supergenes (each color represents a different replicate)
| ParentFreq | ParentW | NonParentW | |
|---|---|---|---|
| parent_supergene_1_summary.txt_1 | 1.1443500 | 1.46189 | 0.670000 |
| parent_supergene_1_summary.txt_2 | 1.1917500 | 1.56757 | 0.826087 |
| parent_supergene_1_summary.txt_3 | 1.1563500 | 1.65963 | 0.628319 |
| parent_supergene_1_summary.txt_4 | 1.1744700 | 1.55932 | 0.682927 |
| parent_supergene_2_summary.txt_1 | 1.1443500 | 1.46189 | 0.670000 |
| parent_supergene_2_summary.txt_2 | 1.1917500 | 1.56757 | 0.826087 |
| parent_supergene_2_summary.txt_3 | 1.1563500 | 1.65963 | 0.628319 |
| parent_supergene_2_summary.txt_4 | 1.1744700 | 1.55932 | 0.682927 |
| parent_supergene_3_summary.txt_1 | 0.0415676 | 1.71264 | 0.492308 |
| parent_supergene_3_summary.txt_2 | 0.0403339 | 1.63820 | 0.441176 |
| parent_supergene_3_summary.txt_3 | 0.0401651 | 1.77017 | 0.710526 |
| parent_supergene_3_summary.txt_4 | 0.0404482 | 1.65455 | 0.691176 |
| parent_supergene_4_summary.txt_1 | 0.0415676 | 1.71264 | 0.492308 |
| parent_supergene_4_summary.txt_2 | 0.0403339 | 1.63820 | 0.441176 |
| parent_supergene_4_summary.txt_3 | 0.0401651 | 1.77017 | 0.710526 |
| parent_supergene_4_summary.txt_4 | 0.0404482 | 1.65455 | 0.691176 |
| parent_supergene_5_summary.txt_1 | 0.0415676 | 1.71264 | 0.492308 |
| parent_supergene_5_summary.txt_2 | 0.0403339 | 1.63820 | 0.441176 |
| parent_supergene_5_summary.txt_3 | 0.0401651 | 1.77017 | 0.710526 |
| parent_supergene_5_summary.txt_4 | 0.0404482 | 1.65455 | 0.691176 |
Variation was maintained in 20 of the 20. 0 of the 20 populations crashed. Of the 20 replicates, 20 reached an equilibrium by 10000 generations.
Let’s look at the trajectories of the parent traits.
Evolution of parenting trait values with a supergene
Frequency of parent morph with supergenes without viability selection (each color represents a different replicate)
| ParentFreq | ParentW | NonParentW | |
|---|---|---|---|
| parent_supergene_novs_1_summary.txt_1 | 0.881092 | 1.62611 | 0.557377 |
| parent_supergene_novs_1_summary.txt_2 | 0.868726 | 1.70000 | 0.558824 |
| parent_supergene_novs_1_summary.txt_3 | 0.855131 | 1.62824 | 0.486111 |
| parent_supergene_novs_1_summary.txt_4 | 0.875740 | 1.62162 | 0.761905 |
| parent_supergene_novs_2_summary.txt_1 | 0.866142 | 1.71136 | 0.779412 |
| parent_supergene_novs_2_summary.txt_2 | 0.875264 | 1.86473 | 0.864407 |
| parent_supergene_novs_2_summary.txt_3 | 0.851301 | 1.53493 | 0.512500 |
| parent_supergene_novs_2_summary.txt_4 | 0.862786 | 1.77108 | 0.560606 |
| parent_supergene_novs_3_summary.txt_1 | 0.860153 | 1.55679 | 0.753425 |
| parent_supergene_novs_3_summary.txt_2 | 0.871743 | 1.69885 | 0.750000 |
| parent_supergene_novs_3_summary.txt_3 | 0.835317 | 1.53682 | 0.759036 |
| parent_supergene_novs_3_summary.txt_4 | 0.835968 | 1.62411 | 0.590361 |
| parent_supergene_novs_4_summary.txt_1 | 0.860153 | 1.55679 | 0.753425 |
| parent_supergene_novs_4_summary.txt_2 | 0.871743 | 1.69885 | 0.750000 |
| parent_supergene_novs_4_summary.txt_3 | 0.835317 | 1.53682 | 0.759036 |
| parent_supergene_novs_4_summary.txt_4 | 0.835968 | 1.62411 | 0.590361 |
| parent_supergene_novs_5_summary.txt_1 | 0.860153 | 1.55679 | 0.753425 |
| parent_supergene_novs_5_summary.txt_2 | 0.871743 | 1.69885 | 0.750000 |
| parent_supergene_novs_5_summary.txt_3 | 0.835317 | 1.53682 | 0.759036 |
| parent_supergene_novs_5_summary.txt_4 | 0.835968 | 1.62411 | 0.590361 |
Variation was maintained in 20 of the 20. 0 of the 20 populations crashed. Of the 20 replicates, 20 reached an equilibrium by 10000 generations.
Let’s look at the trajectories of the parent traits.
Evolution of parenting trait values with a supergene without viability selection
The different runs have different outcomes. To better see this, let’s look at the morph frequencies in each rep separately.
Frequency of the 4 morphs in each rep with supergenes
| Generation | Pop | PopSize | NumMal | NumFem | NumProgeny | ParentThresh | ParentAEmean | ParentAEsd | ParentFreq | ParentW | NonParentW | CourterThresh | CourterAEmean | CourterAEsd | CourterFreq | CourterW | NonCourterW | FreqNcNp | FreqCNp | FreqNcP | FreqCP | PrefThresh | PrefFreq | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| parent-courter_supergene_1_summary.txt_1 | 11999 | Pop0 | 943 | 472 | 471 | 1000 | 0.890749 | 0.442797 | 0.881010 | 0.0753190 | 0 | 0.414449 | -0.942183 | -0.795600 | 1.133670 | 0.557203 | 0.414449 | 0 | 0 | 0.557203 | 0.442797 | 0 | NA | NA |
| parent-courter_supergene_1_summary.txt_2 | 11999 | Pop1 | 944 | 482 | 462 | 1000 | 0.890749 | 0.429461 | 0.881584 | 0.0739243 | 0 | 0.305455 | -0.942183 | -0.804237 | 1.112670 | 0.570539 | 0.305455 | 0 | 0 | 0.570539 | 0.429461 | 0 | NA | NA |
| parent-courter_supergene_1_summary.txt_3 | 11999 | Pop2 | 939 | 471 | 468 | 1000 | 0.890749 | 0.456476 | 0.886884 | 0.0729530 | 0 | 0.312500 | -0.942183 | -0.884011 | 1.098050 | 0.543524 | 0.312500 | 0 | 0 | 0.543524 | 0.456476 | 0 | NA | NA |
| parent-courter_supergene_1_summary.txt_4 | 11999 | Pop3 | 939 | 479 | 460 | 1000 | 0.890749 | 0.430063 | 0.882684 | 0.0733204 | 0 | 0.391941 | -0.942183 | -0.820793 | 1.103580 | 0.569937 | 0.391941 | 0 | 0 | 0.569937 | 0.430063 | 0 | NA | NA |
| parent-courter_supergene_2_summary.txt_1 | 11999 | Pop0 | 943 | 472 | 471 | 1000 | 0.890749 | 0.442797 | 0.881010 | 0.0753190 | 0 | 0.414449 | -0.942183 | -0.795600 | 1.133670 | 0.557203 | 0.414449 | 0 | 0 | 0.557203 | 0.442797 | 0 | NA | NA |
| parent-courter_supergene_2_summary.txt_2 | 11999 | Pop1 | 944 | 482 | 462 | 1000 | 0.890749 | 0.429461 | 0.881584 | 0.0739243 | 0 | 0.305455 | -0.942183 | -0.804237 | 1.112670 | 0.570539 | 0.305455 | 0 | 0 | 0.570539 | 0.429461 | 0 | NA | NA |
| parent-courter_supergene_2_summary.txt_3 | 11999 | Pop2 | 939 | 471 | 468 | 1000 | 0.890749 | 0.456476 | 0.886884 | 0.0729530 | 0 | 0.312500 | -0.942183 | -0.884011 | 1.098050 | 0.543524 | 0.312500 | 0 | 0 | 0.543524 | 0.456476 | 0 | NA | NA |
| parent-courter_supergene_2_summary.txt_4 | 11999 | Pop3 | 939 | 479 | 460 | 1000 | 0.890749 | 0.430063 | 0.882684 | 0.0733204 | 0 | 0.391941 | -0.942183 | -0.820793 | 1.103580 | 0.569937 | 0.391941 | 0 | 0 | 0.569937 | 0.430063 | 0 | NA | NA |
| parent-courter_supergene_3_summary.txt_1 | 11999 | Pop0 | 916 | 439 | 477 | 1000 | -0.396641 | 0.412301 | -0.454427 | 0.5549950 | 0 | 0.426357 | -0.383509 | -0.325517 | 0.556975 | 0.587699 | 0.426357 | 0 | 0 | 0.587699 | 0.412301 | 0 | NA | NA |
| parent-courter_supergene_3_summary.txt_2 | 11999 | Pop1 | 959 | 464 | 495 | 1000 | -0.396641 | 0.418103 | -0.445153 | 0.5536360 | 0 | 0.362963 | -0.383509 | -0.334824 | 0.555611 | 0.581897 | 0.362963 | 0 | 0 | 0.581897 | 0.418103 | 0 | NA | NA |
| parent-courter_supergene_3_summary.txt_3 | 11999 | Pop2 | 939 | 454 | 485 | 1000 | -0.396641 | 0.411894 | -0.442378 | 0.5484150 | 0 | 0.486891 | -0.383509 | -0.337609 | 0.550371 | 0.588106 | 0.486891 | 0 | 0 | 0.588106 | 0.411894 | 0 | NA | NA |
| parent-courter_supergene_3_summary.txt_4 | 11999 | Pop3 | 955 | 469 | 486 | 1000 | -0.396641 | 0.424307 | -0.434795 | 0.5519460 | 0 | 0.292593 | -0.383509 | -0.345219 | 0.553915 | 0.575693 | 0.292593 | 0 | 0 | 0.575693 | 0.424307 | 0 | NA | NA |
| parent-courter_supergene_4_summary.txt_1 | 11999 | Pop0 | 916 | 439 | 477 | 1000 | -0.396641 | 0.412301 | -0.454427 | 0.5549950 | 0 | 0.426357 | -0.383509 | -0.325517 | 0.556975 | 0.587699 | 0.426357 | 0 | 0 | 0.587699 | 0.412301 | 0 | NA | NA |
| parent-courter_supergene_4_summary.txt_2 | 11999 | Pop1 | 959 | 464 | 495 | 1000 | -0.396641 | 0.418103 | -0.445153 | 0.5536360 | 0 | 0.362963 | -0.383509 | -0.334824 | 0.555611 | 0.581897 | 0.362963 | 0 | 0 | 0.581897 | 0.418103 | 0 | NA | NA |
| parent-courter_supergene_4_summary.txt_3 | 11999 | Pop2 | 939 | 454 | 485 | 1000 | -0.396641 | 0.411894 | -0.442378 | 0.5484150 | 0 | 0.486891 | -0.383509 | -0.337609 | 0.550371 | 0.588106 | 0.486891 | 0 | 0 | 0.588106 | 0.411894 | 0 | NA | NA |
| parent-courter_supergene_4_summary.txt_4 | 11999 | Pop3 | 955 | 469 | 486 | 1000 | -0.396641 | 0.424307 | -0.434795 | 0.5519460 | 0 | 0.292593 | -0.383509 | -0.345219 | 0.553915 | 0.575693 | 0.292593 | 0 | 0 | 0.575693 | 0.424307 | 0 | NA | NA |
| parent-courter_supergene_5_summary.txt_1 | 11999 | Pop0 | 916 | 439 | 477 | 1000 | -0.396641 | 0.412301 | -0.454427 | 0.5549950 | 0 | 0.426357 | -0.383509 | -0.325517 | 0.556975 | 0.587699 | 0.426357 | 0 | 0 | 0.587699 | 0.412301 | 0 | NA | NA |
| parent-courter_supergene_5_summary.txt_2 | 11999 | Pop1 | 959 | 464 | 495 | 1000 | -0.396641 | 0.418103 | -0.445153 | 0.5536360 | 0 | 0.362963 | -0.383509 | -0.334824 | 0.555611 | 0.581897 | 0.362963 | 0 | 0 | 0.581897 | 0.418103 | 0 | NA | NA |
| parent-courter_supergene_5_summary.txt_3 | 11999 | Pop2 | 939 | 454 | 485 | 1000 | -0.396641 | 0.411894 | -0.442378 | 0.5484150 | 0 | 0.486891 | -0.383509 | -0.337609 | 0.550371 | 0.588106 | 0.486891 | 0 | 0 | 0.588106 | 0.411894 | 0 | NA | NA |
| parent-courter_supergene_5_summary.txt_4 | 11999 | Pop3 | 955 | 469 | 486 | 1000 | -0.396641 | 0.424307 | -0.434795 | 0.5519460 | 0 | 0.292593 | -0.383509 | -0.345219 | 0.553915 | 0.575693 | 0.292593 | 0 | 0 | 0.575693 | 0.424307 | 0 | NA | NA |
Multiple morphs are maintained in 0 of the 20 replicates, and those morphs contain either a parent or a courter. 0 of those reps with variation went extinct before 10000 generations.
Evolution of the courter and parenting trait values in each rep with a supergene
The different runs have different outcomes. To better see this, let’s look at the morph frequencies in each rep separately.
Frequency of the 4 morphs in each rep with supergenes without viability selection
| Generation | Pop | PopSize | NumMal | NumFem | NumProgeny | ParentThresh | ParentFreq | ParentAEmean | ParentAEsd | ParentW | NonParentW | CourterThresh | CourterFreq | CourterAEmean | CourterAEsd | CourterW | NonCourterW | FreqNcNp | FreqCNp | FreqNcP | FreqCP | PrefThresh | PrefFreq | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| parent-courter_supergene_novs_1_summary.txt_1 | 11999 | Pop0 | 1000 | 539 | 461 | 1000 | -0.125284 | 0.411874 | -0.221956 | 0.8489540 | 0.00000 | 0.198738 | 0.854845 | 0.588126 | 0.883836 | 0.254588 | 0.198738 | 0.00000 | 0.0000000 | 0.588126 | 0.411874 | 0.000000 | NA | NA |
| parent-courter_supergene_novs_1_summary.txt_2 | 11999 | Pop1 | 1000 | 540 | 460 | 1000 | -0.125284 | 0.416667 | -0.225065 | 0.8549870 | 0.00000 | 0.257143 | 0.854845 | 0.583333 | 0.884768 | 0.256397 | 0.257143 | 0.00000 | 0.0000000 | 0.583333 | 0.416667 | 0.000000 | NA | NA |
| parent-courter_supergene_novs_1_summary.txt_3 | 11999 | Pop2 | 1000 | 536 | 464 | 1000 | -0.125284 | 0.421642 | -0.212558 | 0.8529190 | 0.00000 | 0.267742 | 0.854845 | 0.578358 | 0.881017 | 0.255777 | 0.267742 | 0.00000 | 0.0000000 | 0.578358 | 0.421642 | 0.000000 | NA | NA |
| parent-courter_supergene_novs_1_summary.txt_4 | 11999 | Pop3 | 1000 | 536 | 464 | 1000 | -0.125284 | 0.421642 | -0.199379 | 0.8459160 | 0.00000 | 0.293548 | 0.854845 | 0.578358 | 0.877065 | 0.253677 | 0.293548 | 0.00000 | 0.0000000 | 0.578358 | 0.421642 | 0.000000 | NA | NA |
| parent-courter_supergene_novs_2_summary.txt_1 | 11999 | Pop0 | 1000 | 539 | 461 | 1000 | -0.125284 | 0.411874 | -0.221956 | 0.8489540 | 0.00000 | 0.198738 | 0.854845 | 0.588126 | 0.883836 | 0.254588 | 0.198738 | 0.00000 | 0.0000000 | 0.588126 | 0.411874 | 0.000000 | NA | NA |
| parent-courter_supergene_novs_2_summary.txt_2 | 11999 | Pop1 | 1000 | 540 | 460 | 1000 | -0.125284 | 0.416667 | -0.225065 | 0.8549870 | 0.00000 | 0.257143 | 0.854845 | 0.583333 | 0.884768 | 0.256397 | 0.257143 | 0.00000 | 0.0000000 | 0.583333 | 0.416667 | 0.000000 | NA | NA |
| parent-courter_supergene_novs_2_summary.txt_3 | 11999 | Pop2 | 1000 | 536 | 464 | 1000 | -0.125284 | 0.421642 | -0.212558 | 0.8529190 | 0.00000 | 0.267742 | 0.854845 | 0.578358 | 0.881017 | 0.255777 | 0.267742 | 0.00000 | 0.0000000 | 0.578358 | 0.421642 | 0.000000 | NA | NA |
| parent-courter_supergene_novs_2_summary.txt_4 | 11999 | Pop3 | 1000 | 536 | 464 | 1000 | -0.125284 | 0.421642 | -0.199379 | 0.8459160 | 0.00000 | 0.293548 | 0.854845 | 0.578358 | 0.877065 | 0.253677 | 0.293548 | 0.00000 | 0.0000000 | 0.578358 | 0.421642 | 0.000000 | NA | NA |
| parent-courter_supergene_novs_3_summary.txt_1 | 11999 | Pop0 | 944 | 478 | 466 | 1000 | -0.300758 | 0.912134 | -0.226742 | 0.0783806 | 1.93349 | 1.119050 | 1.482630 | 0.912134 | 2.460770 | 1.035820 | 1.933490 | 1.11905 | 0.0878661 | 0.000000 | 0.000000 | 0.912134 | NA | NA |
| parent-courter_supergene_novs_3_summary.txt_2 | 11999 | Pop1 | 945 | 458 | 487 | 1000 | -0.300758 | 0.927948 | -0.225552 | 0.0791775 | 2.03529 | 1.878790 | 1.482630 | 0.927948 | 2.476500 | 1.046350 | 2.035290 | 1.87879 | 0.0720524 | 0.000000 | 0.000000 | 0.927948 | NA | NA |
| parent-courter_supergene_novs_3_summary.txt_3 | 11999 | Pop2 | 1000 | 476 | 524 | 1000 | -0.300758 | 0.888655 | -0.230285 | 0.0783230 | 2.00000 | 1.018870 | 1.482630 | 0.888655 | 2.413950 | 1.035060 | 2.000000 | 1.01887 | 0.1113450 | 0.000000 | 0.000000 | 0.888655 | NA | NA |
| parent-courter_supergene_novs_3_summary.txt_4 | 11999 | Pop3 | 974 | 465 | 509 | 1000 | -0.300758 | 0.909677 | -0.227153 | 0.0783998 | 1.96454 | 1.547620 | 1.482630 | 0.909677 | 2.455350 | 1.036080 | 1.964540 | 1.54762 | 0.0903226 | 0.000000 | 0.000000 | 0.909677 | NA | NA |
| parent-courter_supergene_novs_4_summary.txt_1 | 11999 | Pop0 | 944 | 478 | 466 | 1000 | -0.300758 | 0.912134 | -0.226742 | 0.0783806 | 1.93349 | 1.119050 | 1.482630 | 0.912134 | 2.460770 | 1.035820 | 1.933490 | 1.11905 | 0.0878661 | 0.000000 | 0.000000 | 0.912134 | NA | NA |
| parent-courter_supergene_novs_4_summary.txt_2 | 11999 | Pop1 | 945 | 458 | 487 | 1000 | -0.300758 | 0.927948 | -0.225552 | 0.0791775 | 2.03529 | 1.878790 | 1.482630 | 0.927948 | 2.476500 | 1.046350 | 2.035290 | 1.87879 | 0.0720524 | 0.000000 | 0.000000 | 0.927948 | NA | NA |
| parent-courter_supergene_novs_4_summary.txt_3 | 11999 | Pop2 | 1000 | 476 | 524 | 1000 | -0.300758 | 0.888655 | -0.230285 | 0.0783230 | 2.00000 | 1.018870 | 1.482630 | 0.888655 | 2.413950 | 1.035060 | 2.000000 | 1.01887 | 0.1113450 | 0.000000 | 0.000000 | 0.888655 | NA | NA |
| parent-courter_supergene_novs_4_summary.txt_4 | 11999 | Pop3 | 974 | 465 | 509 | 1000 | -0.300758 | 0.909677 | -0.227153 | 0.0783998 | 1.96454 | 1.547620 | 1.482630 | 0.909677 | 2.455350 | 1.036080 | 1.964540 | 1.54762 | 0.0903226 | 0.000000 | 0.000000 | 0.909677 | NA | NA |
| parent-courter_supergene_novs_5_summary.txt_1 | 11999 | Pop0 | 944 | 478 | 466 | 1000 | -0.300758 | 0.912134 | -0.226742 | 0.0783806 | 1.93349 | 1.119050 | 1.482630 | 0.912134 | 2.460770 | 1.035820 | 1.933490 | 1.11905 | 0.0878661 | 0.000000 | 0.000000 | 0.912134 | NA | NA |
| parent-courter_supergene_novs_5_summary.txt_2 | 11999 | Pop1 | 945 | 458 | 487 | 1000 | -0.300758 | 0.927948 | -0.225552 | 0.0791775 | 2.03529 | 1.878790 | 1.482630 | 0.927948 | 2.476500 | 1.046350 | 2.035290 | 1.87879 | 0.0720524 | 0.000000 | 0.000000 | 0.927948 | NA | NA |
| parent-courter_supergene_novs_5_summary.txt_3 | 11999 | Pop2 | 1000 | 476 | 524 | 1000 | -0.300758 | 0.888655 | -0.230285 | 0.0783230 | 2.00000 | 1.018870 | 1.482630 | 0.888655 | 2.413950 | 1.035060 | 2.000000 | 1.01887 | 0.1113450 | 0.000000 | 0.000000 | 0.888655 | NA | NA |
| parent-courter_supergene_novs_5_summary.txt_4 | 11999 | Pop3 | 974 | 465 | 509 | 1000 | -0.300758 | 0.909677 | -0.227153 | 0.0783998 | 1.96454 | 1.547620 | 1.482630 | 0.909677 | 2.455350 | 1.036080 | 1.964540 | 1.54762 | 0.0903226 | 0.000000 | 0.000000 | 0.909677 | NA | NA |
Multiple morphs are maintained in 20 of the 20 replicates, and those morphs contain either a parent or a courter. 0 of those reps with variation went extinct before 10000 generations.
Evolution of the courter and parenting trait values in each rep with a supergene without viability selection